Multiple sequence alignment - TraesCS7D01G531400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G531400 chr7D 100.000 3477 0 0 1 3477 625609329 625612805 0.000000e+00 6421
1 TraesCS7D01G531400 chr7D 91.509 106 7 1 1551 1656 625651181 625651284 1.010000e-30 145
2 TraesCS7D01G531400 chr7D 93.258 89 3 2 1365 1453 625855258 625855173 1.010000e-25 128
3 TraesCS7D01G531400 chr7D 89.423 104 6 1 1551 1654 625855033 625854935 3.640000e-25 126
4 TraesCS7D01G531400 chr7D 94.805 77 4 0 1377 1453 625650956 625651032 1.700000e-23 121
5 TraesCS7D01G531400 chr7D 96.774 62 2 0 2261 2322 625651582 625651643 1.710000e-18 104
6 TraesCS7D01G531400 chr7A 92.514 1269 70 11 1993 3243 721205862 721207123 0.000000e+00 1794
7 TraesCS7D01G531400 chr7A 92.611 609 40 4 851 1455 721204657 721205264 0.000000e+00 870
8 TraesCS7D01G531400 chr7A 84.127 504 33 18 1508 1998 721205357 721205826 8.860000e-121 444
9 TraesCS7D01G531400 chr7A 94.595 222 11 1 528 749 721181391 721181611 3.320000e-90 342
10 TraesCS7D01G531400 chr7A 91.129 248 19 3 3232 3477 721212308 721212554 2.000000e-87 333
11 TraesCS7D01G531400 chr7A 92.093 215 16 1 528 742 721204342 721204555 5.640000e-78 302
12 TraesCS7D01G531400 chr7A 91.358 81 6 1 1551 1631 721223099 721223178 3.670000e-20 110
13 TraesCS7D01G531400 chr7A 95.312 64 3 0 2261 2324 721223334 721223397 6.140000e-18 102
14 TraesCS7D01G531400 chr7B 86.957 1058 86 19 1 1051 682382905 682381893 0.000000e+00 1142
15 TraesCS7D01G531400 chr7B 89.822 845 62 13 614 1453 682379462 682378637 0.000000e+00 1062
16 TraesCS7D01G531400 chr7B 87.205 891 81 13 590 1472 725186573 725185708 0.000000e+00 983
17 TraesCS7D01G531400 chr7B 94.030 469 15 3 1499 1967 725185566 725185111 0.000000e+00 699
18 TraesCS7D01G531400 chr7B 88.160 549 33 17 1993 2512 725185042 725184497 2.950000e-175 625
19 TraesCS7D01G531400 chr7B 85.959 584 44 9 2648 3225 725184453 725183902 1.070000e-164 590
20 TraesCS7D01G531400 chr7B 83.276 580 65 18 2065 2622 682378060 682377491 4.010000e-139 505
21 TraesCS7D01G531400 chr7B 80.876 502 65 17 24 507 682380926 682380438 1.970000e-97 366
22 TraesCS7D01G531400 chr7B 88.772 285 20 5 1704 1986 682378346 682378072 4.300000e-89 339
23 TraesCS7D01G531400 chr7B 81.931 404 36 13 753 1147 725187668 725187293 1.210000e-79 307
24 TraesCS7D01G531400 chr7B 77.798 554 70 34 2635 3174 682376143 682375629 3.390000e-75 292
25 TraesCS7D01G531400 chr7B 91.925 161 10 2 581 740 725187896 725187738 4.520000e-54 222
26 TraesCS7D01G531400 chr7B 99.057 106 1 0 1527 1632 682378468 682378363 1.270000e-44 191
27 TraesCS7D01G531400 chr7B 90.909 143 11 1 590 732 725195553 725195413 1.270000e-44 191
28 TraesCS7D01G531400 chr7B 91.129 124 8 2 755 878 725189988 725189868 7.720000e-37 165
29 TraesCS7D01G531400 chr7B 87.970 133 13 3 465 596 725186751 725186621 1.670000e-33 154
30 TraesCS7D01G531400 chr7B 87.970 133 13 3 465 596 725195728 725195598 1.670000e-33 154
31 TraesCS7D01G531400 chr7B 98.667 75 1 0 2885 2959 725181586 725181512 2.180000e-27 134
32 TraesCS7D01G531400 chr7B 93.103 87 6 0 1367 1453 725605224 725605310 1.010000e-25 128
33 TraesCS7D01G531400 chr7B 93.103 87 6 0 1367 1453 725640819 725640905 1.010000e-25 128
34 TraesCS7D01G531400 chr7B 94.030 67 3 1 2259 2324 682355101 682355035 2.210000e-17 100
35 TraesCS7D01G531400 chr7B 75.652 230 40 11 2107 2324 725605550 725605775 2.210000e-17 100
36 TraesCS7D01G531400 chrUn 88.235 765 52 15 723 1472 87746480 87747221 0.000000e+00 880
37 TraesCS7D01G531400 chrUn 90.486 494 29 6 1501 1986 87747365 87747848 1.360000e-178 636
38 TraesCS7D01G531400 chrUn 82.370 692 75 32 2050 2713 87747845 87748517 3.030000e-155 558
39 TraesCS7D01G531400 chrUn 86.835 357 35 5 68 422 343484544 343484890 4.210000e-104 388
40 TraesCS7D01G531400 chrUn 93.636 220 13 1 3258 3477 343485294 343485512 9.310000e-86 327
41 TraesCS7D01G531400 chrUn 93.103 87 6 0 1367 1453 332189883 332189797 1.010000e-25 128
42 TraesCS7D01G531400 chrUn 75.652 230 40 11 2107 2324 332189557 332189332 2.210000e-17 100
43 TraesCS7D01G531400 chr6A 85.024 207 20 5 803 1005 74384012 74383813 2.120000e-47 200


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G531400 chr7D 625609329 625612805 3476 False 6421.000000 6421 100.000000 1 3477 1 chr7D.!!$F1 3476
1 TraesCS7D01G531400 chr7A 721204342 721207123 2781 False 852.500000 1794 90.336250 528 3243 4 chr7A.!!$F3 2715
2 TraesCS7D01G531400 chr7B 682375629 682382905 7276 True 556.714286 1142 86.651143 1 3174 7 chr7B.!!$R2 3173
3 TraesCS7D01G531400 chr7B 725181512 725189988 8476 True 431.000000 983 89.664000 465 3225 9 chr7B.!!$R3 2760
4 TraesCS7D01G531400 chrUn 87746480 87748517 2037 False 691.333333 880 87.030333 723 2713 3 chrUn.!!$F1 1990
5 TraesCS7D01G531400 chrUn 343484544 343485512 968 False 357.500000 388 90.235500 68 3477 2 chrUn.!!$F2 3409

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
849 3721 0.037877 ACCGACGAAGAAGAGGGAGA 59.962 55.0 0.00 0.0 0.00 3.71 F
2197 8279 0.041047 TCGTACGTCTTCCACACACG 60.041 55.0 16.05 0.0 39.48 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 8363 0.329261 CACTTTGGCATCCCTGGAGA 59.671 55.0 0.0 0.0 0.0 3.71 R
3252 10844 0.038251 GCTTGCCTTTTTCCTTCCCG 60.038 55.0 0.0 0.0 0.0 5.14 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 7.993821 TTTGAAAATAGTTCACGCATTTGAA 57.006 28.000 0.00 0.00 32.94 2.69
47 48 7.993821 TTGAAAATAGTTCACGCATTTGAAA 57.006 28.000 0.00 0.00 37.24 2.69
48 49 7.993821 TGAAAATAGTTCACGCATTTGAAAA 57.006 28.000 0.00 0.00 37.24 2.29
50 51 7.489435 TGAAAATAGTTCACGCATTTGAAAACA 59.511 29.630 0.00 0.00 37.24 2.83
51 52 7.763172 AAATAGTTCACGCATTTGAAAACAA 57.237 28.000 0.00 0.00 37.24 2.83
53 54 7.945033 ATAGTTCACGCATTTGAAAACAAAT 57.055 28.000 0.00 0.00 37.24 2.32
164 170 5.016831 ACAAAGAAAACCAGAGAAACCACT 58.983 37.500 0.00 0.00 0.00 4.00
204 210 2.017668 ATGTCCCCCAAACCAGTGCA 62.018 55.000 0.00 0.00 0.00 4.57
223 230 0.252467 ACTGTGCTAGGGAGAGGCTT 60.252 55.000 0.00 0.00 0.00 4.35
287 294 9.274206 AGGTTACTAAACTGAGAAAAGTTCATC 57.726 33.333 0.00 0.00 39.48 2.92
381 388 1.789523 ATAGGCCTACTCCGAAAGCA 58.210 50.000 16.61 0.00 0.00 3.91
425 433 3.149899 GGATGCATATCAGCCCGAG 57.850 57.895 0.00 0.00 45.34 4.63
460 472 1.134075 CATGCAGCGAGTGAGTTGC 59.866 57.895 0.00 0.00 46.39 4.17
473 3247 0.380378 GAGTTGCGCAGAAACCAACA 59.620 50.000 11.31 0.00 40.85 3.33
491 3265 4.320202 CCAACAAACGAAATGACCTACCTG 60.320 45.833 0.00 0.00 0.00 4.00
496 3270 1.406069 CGAAATGACCTACCTGCTGCT 60.406 52.381 0.00 0.00 0.00 4.24
524 3298 0.104487 AGCAGAGATGCATGTCTCCG 59.896 55.000 22.65 14.05 44.55 4.63
529 3303 3.686241 CAGAGATGCATGTCTCCGAAAAA 59.314 43.478 22.65 0.00 44.55 1.94
531 3305 4.946157 AGAGATGCATGTCTCCGAAAAATT 59.054 37.500 20.07 0.00 44.55 1.82
540 3314 3.057596 GTCTCCGAAAAATTGGTCATGCA 60.058 43.478 0.00 0.00 0.00 3.96
541 3315 3.571828 TCTCCGAAAAATTGGTCATGCAA 59.428 39.130 0.00 0.00 0.00 4.08
596 3370 3.927142 GGACATTGTTCAGGACTACTTCG 59.073 47.826 0.00 0.00 0.00 3.79
682 3508 0.251297 TCTCCCCAAACCATGTGCAG 60.251 55.000 0.00 0.00 0.00 4.41
745 3581 6.379386 GTTTCCCTTCTGTTATTGTTACAGC 58.621 40.000 0.00 0.00 42.12 4.40
776 3643 1.668628 GCAGGCAAAACGTACCATTGG 60.669 52.381 0.00 0.00 0.00 3.16
835 3702 5.721232 CCAGATTTCCATAGGTATACCGAC 58.279 45.833 16.31 0.00 42.08 4.79
849 3721 0.037877 ACCGACGAAGAAGAGGGAGA 59.962 55.000 0.00 0.00 0.00 3.71
878 3750 2.415983 TGGAAACTCTCCTCCCTTCA 57.584 50.000 0.00 0.00 45.64 3.02
879 3751 2.701551 TGGAAACTCTCCTCCCTTCAA 58.298 47.619 0.00 0.00 45.64 2.69
888 3763 1.923148 TCCTCCCTTCAATTCCTTCCC 59.077 52.381 0.00 0.00 0.00 3.97
891 3766 1.923148 TCCCTTCAATTCCTTCCCCTC 59.077 52.381 0.00 0.00 0.00 4.30
895 3770 3.956848 CCTTCAATTCCTTCCCCTCATTC 59.043 47.826 0.00 0.00 0.00 2.67
896 3771 3.669939 TCAATTCCTTCCCCTCATTCC 57.330 47.619 0.00 0.00 0.00 3.01
989 6720 4.849329 GCCGCGACCGAGACGATT 62.849 66.667 8.23 0.00 36.29 3.34
1139 6874 0.457853 TTCGGTTCCGATCTGCTTCG 60.458 55.000 14.70 0.00 38.30 3.79
1238 6976 3.062466 CTCGGCTCCGTCAGGTCA 61.062 66.667 8.28 0.00 40.74 4.02
1287 7025 1.416401 TCGGATGACAGGGCTTTATCC 59.584 52.381 0.00 0.00 35.16 2.59
1289 7027 1.543429 GGATGACAGGGCTTTATCCGG 60.543 57.143 0.00 0.00 0.00 5.14
1455 7193 2.477525 GCTACCTCGACGTCAGGTAAAG 60.478 54.545 29.90 25.39 44.38 1.85
1473 7296 5.690857 GGTAAAGACTGTACTGTCAACTGAC 59.309 44.000 28.08 18.84 44.97 3.51
1474 7297 5.599999 AAAGACTGTACTGTCAACTGACT 57.400 39.130 28.08 8.71 44.99 3.41
1497 7320 5.940617 TGAGAGAAAAATTCAGTTCCCTGA 58.059 37.500 0.00 0.00 45.95 3.86
1548 7458 2.574006 TTGCTGATGCCTTGTCTCTT 57.426 45.000 0.00 0.00 38.71 2.85
1633 7543 1.429148 GCACCGGCTCAGGTAATTCG 61.429 60.000 0.00 0.00 43.89 3.34
1674 7591 0.689623 CCAGTGAAGCTCCCTCTTGT 59.310 55.000 0.00 0.00 0.00 3.16
1675 7592 1.610102 CCAGTGAAGCTCCCTCTTGTG 60.610 57.143 0.00 0.00 0.00 3.33
1676 7593 1.071385 CAGTGAAGCTCCCTCTTGTGT 59.929 52.381 0.00 0.00 0.00 3.72
1677 7594 1.346068 AGTGAAGCTCCCTCTTGTGTC 59.654 52.381 0.00 0.00 0.00 3.67
1678 7595 1.346068 GTGAAGCTCCCTCTTGTGTCT 59.654 52.381 0.00 0.00 0.00 3.41
1679 7596 2.050144 TGAAGCTCCCTCTTGTGTCTT 58.950 47.619 0.00 0.00 0.00 3.01
1680 7597 2.224378 TGAAGCTCCCTCTTGTGTCTTG 60.224 50.000 0.00 0.00 0.00 3.02
1804 7726 3.466836 TCAGAATATGAACATCCGCACC 58.533 45.455 0.00 0.00 34.02 5.01
1805 7727 3.118445 TCAGAATATGAACATCCGCACCA 60.118 43.478 0.00 0.00 34.02 4.17
1806 7728 3.627123 CAGAATATGAACATCCGCACCAA 59.373 43.478 0.00 0.00 0.00 3.67
1967 7899 0.249398 AGGAGCATTTTACGGACGCT 59.751 50.000 0.00 0.00 35.14 5.07
1976 7912 1.286501 TTACGGACGCTGATGAATGC 58.713 50.000 0.00 0.00 0.00 3.56
1982 7918 3.058708 CGGACGCTGATGAATGCATAATT 60.059 43.478 0.00 0.00 34.11 1.40
1983 7919 4.224433 GGACGCTGATGAATGCATAATTG 58.776 43.478 0.00 0.00 34.11 2.32
1985 7921 4.852138 ACGCTGATGAATGCATAATTGTC 58.148 39.130 0.00 0.00 34.11 3.18
1987 7923 5.759763 ACGCTGATGAATGCATAATTGTCTA 59.240 36.000 0.00 0.00 34.11 2.59
1991 7966 8.912658 GCTGATGAATGCATAATTGTCTAATTG 58.087 33.333 0.00 0.00 37.12 2.32
2017 7992 8.455682 GTCTATCACTATTCACTAGCTACATCC 58.544 40.741 0.00 0.00 0.00 3.51
2021 7996 8.023021 TCACTATTCACTAGCTACATCCAAAT 57.977 34.615 0.00 0.00 0.00 2.32
2028 8004 5.882557 CACTAGCTACATCCAAATCCAAGTT 59.117 40.000 0.00 0.00 0.00 2.66
2035 8011 4.021719 ACATCCAAATCCAAGTTGCTTCAG 60.022 41.667 0.00 0.00 0.00 3.02
2040 8016 3.777106 ATCCAAGTTGCTTCAGAGTGA 57.223 42.857 0.00 0.00 0.00 3.41
2085 8167 5.729510 GAAGTTTACCTTCTCTGCTCTGAT 58.270 41.667 0.00 0.00 45.19 2.90
2086 8168 5.337578 AGTTTACCTTCTCTGCTCTGATC 57.662 43.478 0.00 0.00 0.00 2.92
2125 8207 1.631405 CAGGGATGGCCAAAAACTCA 58.369 50.000 10.96 0.00 35.15 3.41
2196 8278 1.983605 CATCGTACGTCTTCCACACAC 59.016 52.381 16.05 0.00 0.00 3.82
2197 8279 0.041047 TCGTACGTCTTCCACACACG 60.041 55.000 16.05 0.00 39.48 4.49
2199 8281 1.007038 TACGTCTTCCACACACGCC 60.007 57.895 0.00 0.00 37.02 5.68
2200 8282 2.424705 TACGTCTTCCACACACGCCC 62.425 60.000 0.00 0.00 37.02 6.13
2201 8283 2.668550 GTCTTCCACACACGCCCC 60.669 66.667 0.00 0.00 0.00 5.80
2585 8812 3.119291 CGTCTTGATCTCGGATTCAAGG 58.881 50.000 21.21 9.84 45.69 3.61
2674 10237 8.970691 ATGTTAGCACAACAAAAGATTATGAC 57.029 30.769 7.83 0.00 36.16 3.06
2680 10243 6.381801 CACAACAAAAGATTATGACCCTGTC 58.618 40.000 0.00 0.00 0.00 3.51
2736 10305 9.739276 TGTGTAAAACCTAATCTGATCAGAATT 57.261 29.630 28.40 22.26 41.36 2.17
2806 10390 1.407936 ACAGCTCACAGTGACAGAGT 58.592 50.000 0.00 0.00 0.00 3.24
2807 10391 2.587522 ACAGCTCACAGTGACAGAGTA 58.412 47.619 0.00 0.00 0.00 2.59
3021 10608 9.498307 AAGAAATTAACCGCATTAGAATAAACG 57.502 29.630 0.00 0.00 0.00 3.60
3033 10620 2.819608 AGAATAAACGCACTTGCCATGT 59.180 40.909 0.00 0.00 37.91 3.21
3041 10628 2.278854 GCACTTGCCATGTGTTTGTTT 58.721 42.857 11.78 0.00 37.70 2.83
3094 10681 2.324215 CATCCACAATGCTAGGCGG 58.676 57.895 0.00 0.00 0.00 6.13
3101 10688 2.545526 CACAATGCTAGGCGGTTATCTG 59.454 50.000 0.00 0.00 0.00 2.90
3161 10749 2.393271 AAATCTCAACGCCCTCTCAG 57.607 50.000 0.00 0.00 0.00 3.35
3163 10751 0.534412 ATCTCAACGCCCTCTCAGTG 59.466 55.000 0.00 0.00 0.00 3.66
3244 10836 7.441458 ACACTAATATATCTTCGGAACAAAGGC 59.559 37.037 0.00 0.00 0.00 4.35
3245 10837 7.441157 CACTAATATATCTTCGGAACAAAGGCA 59.559 37.037 0.00 0.00 0.00 4.75
3246 10838 7.990886 ACTAATATATCTTCGGAACAAAGGCAA 59.009 33.333 0.00 0.00 0.00 4.52
3248 10840 1.314730 TCTTCGGAACAAAGGCAACC 58.685 50.000 0.00 0.00 37.17 3.77
3249 10841 0.040425 CTTCGGAACAAAGGCAACCG 60.040 55.000 0.00 0.00 44.09 4.44
3250 10842 0.748729 TTCGGAACAAAGGCAACCGT 60.749 50.000 0.00 0.00 43.36 4.83
3252 10844 0.317519 CGGAACAAAGGCAACCGTTC 60.318 55.000 0.00 0.00 39.03 3.95
3253 10845 0.317519 GGAACAAAGGCAACCGTTCG 60.318 55.000 0.00 0.00 40.05 3.95
3254 10846 0.317519 GAACAAAGGCAACCGTTCGG 60.318 55.000 9.81 9.81 33.03 4.30
3255 10847 1.730451 AACAAAGGCAACCGTTCGGG 61.730 55.000 15.66 0.00 43.62 5.14
3256 10848 1.894756 CAAAGGCAACCGTTCGGGA 60.895 57.895 15.66 0.00 39.97 5.14
3260 10852 2.031465 GCAACCGTTCGGGAAGGA 59.969 61.111 15.66 0.00 39.97 3.36
3331 11682 1.620524 CCCTGGGAATCAAAGGTGCAT 60.621 52.381 7.01 0.00 0.00 3.96
3336 11687 3.006752 TGGGAATCAAAGGTGCATTTGTC 59.993 43.478 11.50 4.40 40.36 3.18
3342 11693 1.086696 AAGGTGCATTTGTCGATCGG 58.913 50.000 16.41 0.00 0.00 4.18
3398 12270 1.227176 GCGTCGGATCCACCCTTAC 60.227 63.158 13.41 0.00 34.64 2.34
3414 12286 2.292016 CCTTACGGTTGTGTGCATCAAA 59.708 45.455 8.46 0.00 0.00 2.69
3416 12288 1.098869 ACGGTTGTGTGCATCAAACA 58.901 45.000 18.04 6.85 32.72 2.83
3456 12832 9.949174 ACATTGCCTTATTTTGAATTTGTTTTC 57.051 25.926 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 8.698854 TCAAATGCGTGAACTATTTTCAAATTC 58.301 29.630 0.00 0.00 0.00 2.17
164 170 3.524095 TTCCCTCTGGATTTTTGCAGA 57.476 42.857 0.00 0.00 41.40 4.26
204 210 0.252467 AAGCCTCTCCCTAGCACAGT 60.252 55.000 0.00 0.00 0.00 3.55
223 230 2.642183 TAACAGGCCGGCCCAAAACA 62.642 55.000 41.72 19.55 36.58 2.83
395 403 3.372730 GCATCCAACTTGGCGGCA 61.373 61.111 7.97 7.97 37.47 5.69
422 430 1.004080 CCTCATGCTATGCCCCTCG 60.004 63.158 0.00 0.00 0.00 4.63
425 433 2.282745 GGCCTCATGCTATGCCCC 60.283 66.667 0.00 0.00 40.92 5.80
460 472 2.181426 TTCGTTTGTTGGTTTCTGCG 57.819 45.000 0.00 0.00 0.00 5.18
461 473 4.026886 GTCATTTCGTTTGTTGGTTTCTGC 60.027 41.667 0.00 0.00 0.00 4.26
473 3247 3.074412 CAGCAGGTAGGTCATTTCGTTT 58.926 45.455 0.00 0.00 0.00 3.60
524 3298 5.634859 ACTCGATTTGCATGACCAATTTTTC 59.365 36.000 0.00 0.00 0.00 2.29
529 3303 3.346315 TGACTCGATTTGCATGACCAAT 58.654 40.909 0.00 0.00 0.00 3.16
531 3305 2.289631 ACTGACTCGATTTGCATGACCA 60.290 45.455 0.00 0.00 0.00 4.02
540 3314 1.611977 TGACCGTGACTGACTCGATTT 59.388 47.619 3.40 0.00 37.64 2.17
541 3315 1.244816 TGACCGTGACTGACTCGATT 58.755 50.000 3.40 0.00 37.64 3.34
596 3370 1.228552 TGGGAAGAAAGCTGCACCC 60.229 57.895 1.02 12.10 35.06 4.61
655 3481 3.433306 TGGTTTGGGGAGACAGTTATG 57.567 47.619 0.00 0.00 0.00 1.90
682 3508 1.310904 TCCAACGTTAACCTTGCACC 58.689 50.000 0.00 0.00 0.00 5.01
745 3581 2.042686 TTTGCCTGCTAGCCAGTATG 57.957 50.000 13.29 0.00 40.06 2.39
751 3618 0.446616 GTACGTTTTGCCTGCTAGCC 59.553 55.000 13.29 0.00 0.00 3.93
776 3643 6.363473 CCTATTTATTCGCGATTGGAGAAAC 58.637 40.000 10.88 0.00 37.98 2.78
788 3655 0.948678 TTGGGCGCCTATTTATTCGC 59.051 50.000 28.56 5.64 45.99 4.70
835 3702 4.258702 TGAAGTTTCTCCCTCTTCTTCG 57.741 45.455 0.00 0.00 38.52 3.79
878 3750 1.410224 GCGGAATGAGGGGAAGGAATT 60.410 52.381 0.00 0.00 0.00 2.17
879 3751 0.183731 GCGGAATGAGGGGAAGGAAT 59.816 55.000 0.00 0.00 0.00 3.01
888 3763 2.190578 GGACTGGGCGGAATGAGG 59.809 66.667 0.00 0.00 0.00 3.86
989 6720 2.821546 CCGACGCCATTTTATCTCTCA 58.178 47.619 0.00 0.00 0.00 3.27
1081 6812 6.267014 GGTTGTATAGATACTTACCTGCAGGA 59.733 42.308 39.19 19.62 36.56 3.86
1139 6874 1.996191 GTCAGATTTGAGACGGAGCAC 59.004 52.381 0.00 0.00 32.98 4.40
1238 6976 0.676184 CCCGATCGATCACCATGACT 59.324 55.000 24.40 0.00 0.00 3.41
1270 7008 1.884235 CCGGATAAAGCCCTGTCATC 58.116 55.000 0.00 0.00 0.00 2.92
1280 7018 4.056050 AGCGTGTAAATAGCCGGATAAAG 58.944 43.478 5.05 0.00 0.00 1.85
1287 7025 2.222953 GGAACAAGCGTGTAAATAGCCG 60.223 50.000 5.50 0.00 36.80 5.52
1289 7027 4.392138 AGAAGGAACAAGCGTGTAAATAGC 59.608 41.667 5.50 0.00 36.80 2.97
1548 7458 1.874345 GAACTCGCCCTCCGTTCTGA 61.874 60.000 0.00 0.00 38.35 3.27
1633 7543 5.710099 TGGAGTGAAGTGGGTTTGATTAATC 59.290 40.000 8.60 8.60 0.00 1.75
1674 7591 9.942850 TGTATTTCTTTCTATGATCACAAGACA 57.057 29.630 8.72 3.13 0.00 3.41
1678 7595 9.123902 CCCATGTATTTCTTTCTATGATCACAA 57.876 33.333 0.00 0.00 0.00 3.33
1679 7596 8.493607 TCCCATGTATTTCTTTCTATGATCACA 58.506 33.333 0.00 0.00 0.00 3.58
1680 7597 8.778358 GTCCCATGTATTTCTTTCTATGATCAC 58.222 37.037 0.00 0.00 0.00 3.06
1699 7619 1.679680 CTTGCTAGCATTGGTCCCATG 59.320 52.381 20.13 0.00 0.00 3.66
1883 7807 3.187227 GCGCCAATAGAGACACCATAATG 59.813 47.826 0.00 0.00 0.00 1.90
1967 7899 9.955208 GACAATTAGACAATTATGCATTCATCA 57.045 29.630 3.54 0.00 32.96 3.07
1991 7966 8.455682 GGATGTAGCTAGTGAATAGTGATAGAC 58.544 40.741 0.00 0.00 33.65 2.59
2011 7986 5.076182 TGAAGCAACTTGGATTTGGATGTA 58.924 37.500 0.00 0.00 0.00 2.29
2017 7992 4.276678 TCACTCTGAAGCAACTTGGATTTG 59.723 41.667 0.00 0.00 0.00 2.32
2021 7996 3.405831 CATCACTCTGAAGCAACTTGGA 58.594 45.455 0.00 0.00 0.00 3.53
2028 8004 1.078918 CCCGCATCACTCTGAAGCA 60.079 57.895 0.92 0.00 40.74 3.91
2035 8011 2.182842 GGACATGCCCGCATCACTC 61.183 63.158 0.00 0.00 33.90 3.51
2040 8016 2.124151 GGAAGGACATGCCCGCAT 60.124 61.111 0.00 0.00 37.37 4.73
2082 8164 8.859236 TGCCAATGGAAATTTAAATTTGATCA 57.141 26.923 26.69 20.70 38.64 2.92
2085 8167 6.658391 CCCTGCCAATGGAAATTTAAATTTGA 59.342 34.615 26.69 15.16 38.64 2.69
2086 8168 6.658391 TCCCTGCCAATGGAAATTTAAATTTG 59.342 34.615 26.69 14.64 38.64 2.32
2125 8207 3.555168 CCGACACTTGCTCTAGAAAACCT 60.555 47.826 0.00 0.00 0.00 3.50
2256 8363 0.329261 CACTTTGGCATCCCTGGAGA 59.671 55.000 0.00 0.00 0.00 3.71
2360 8579 3.681897 CACATGACAGAGAGCAGTTTACC 59.318 47.826 0.00 0.00 0.00 2.85
2613 8841 6.934645 TCCTATACATAAATGGCAAGCTACAC 59.065 38.462 0.00 0.00 0.00 2.90
2664 10227 7.074237 AGGAATATTGGACAGGGTCATAATCTT 59.926 37.037 0.00 0.00 33.68 2.40
2674 10237 4.150897 TCGAAAGGAATATTGGACAGGG 57.849 45.455 0.00 0.00 0.00 4.45
2680 10243 4.823989 AGAAGGCATCGAAAGGAATATTGG 59.176 41.667 0.00 0.00 0.00 3.16
2736 10305 6.658816 TGGCAAGATAGATCACAGCTTAAAAA 59.341 34.615 0.00 0.00 0.00 1.94
2806 10390 3.990959 TCAGTGCCCACATTGTGTATA 57.009 42.857 15.34 0.00 35.19 1.47
2807 10391 2.877097 TCAGTGCCCACATTGTGTAT 57.123 45.000 15.34 0.00 35.19 2.29
3007 10591 3.791353 GGCAAGTGCGTTTATTCTAATGC 59.209 43.478 0.00 0.00 43.26 3.56
3021 10608 1.938625 AACAAACACATGGCAAGTGC 58.061 45.000 21.60 0.00 40.59 4.40
3033 10620 6.148645 ACATCATGCAGTATCGTAAACAAACA 59.851 34.615 0.00 0.00 0.00 2.83
3041 10628 5.006649 GCTTCAAACATCATGCAGTATCGTA 59.993 40.000 0.00 0.00 0.00 3.43
3094 10681 2.037251 TCTCCATAAGCGGCCAGATAAC 59.963 50.000 2.24 0.00 0.00 1.89
3101 10688 1.459450 TGTTTTCTCCATAAGCGGCC 58.541 50.000 0.00 0.00 0.00 6.13
3175 10763 1.201429 ATGAGAGGGGGCTTTCACGT 61.201 55.000 0.00 0.00 0.00 4.49
3213 10805 6.268825 TCCGAAGATATATTAGTGTCTGCC 57.731 41.667 0.00 0.00 0.00 4.85
3244 10836 1.310904 TTTTCCTTCCCGAACGGTTG 58.689 50.000 12.23 0.00 0.00 3.77
3245 10837 1.951602 CTTTTTCCTTCCCGAACGGTT 59.048 47.619 12.23 0.00 0.00 4.44
3246 10838 1.601166 CTTTTTCCTTCCCGAACGGT 58.399 50.000 12.23 0.00 0.00 4.83
3248 10840 0.240145 GCCTTTTTCCTTCCCGAACG 59.760 55.000 0.00 0.00 0.00 3.95
3249 10841 1.324383 TGCCTTTTTCCTTCCCGAAC 58.676 50.000 0.00 0.00 0.00 3.95
3250 10842 1.960689 CTTGCCTTTTTCCTTCCCGAA 59.039 47.619 0.00 0.00 0.00 4.30
3252 10844 0.038251 GCTTGCCTTTTTCCTTCCCG 60.038 55.000 0.00 0.00 0.00 5.14
3253 10845 0.321671 GGCTTGCCTTTTTCCTTCCC 59.678 55.000 4.11 0.00 0.00 3.97
3254 10846 0.321671 GGGCTTGCCTTTTTCCTTCC 59.678 55.000 11.71 0.00 0.00 3.46
3255 10847 1.273606 GAGGGCTTGCCTTTTTCCTTC 59.726 52.381 11.71 0.00 0.00 3.46
3256 10848 1.342074 GAGGGCTTGCCTTTTTCCTT 58.658 50.000 11.71 0.00 0.00 3.36
3260 10852 2.169144 GCATATGAGGGCTTGCCTTTTT 59.831 45.455 6.97 0.00 0.00 1.94
3310 11661 0.972471 GCACCTTTGATTCCCAGGGG 60.972 60.000 5.33 0.92 33.76 4.79
3322 11673 1.468520 CCGATCGACAAATGCACCTTT 59.531 47.619 18.66 0.00 0.00 3.11
3331 11682 3.132289 AGATTTCCTAGCCGATCGACAAA 59.868 43.478 18.66 1.59 0.00 2.83
3336 11687 4.035278 GGATAGATTTCCTAGCCGATCG 57.965 50.000 8.51 8.51 43.26 3.69
3398 12270 1.851666 GTTGTTTGATGCACACAACCG 59.148 47.619 15.12 0.00 44.35 4.44
3414 12286 3.284449 GTCCGGCCTTTGCGTTGT 61.284 61.111 0.00 0.00 38.85 3.32
3416 12288 1.901464 AATGTCCGGCCTTTGCGTT 60.901 52.632 0.00 0.00 38.85 4.84
3456 12832 2.636830 ACCGAAGATGAGATTGCTTGG 58.363 47.619 0.00 0.00 0.00 3.61


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.